Hey
I am not sure if you are messing up with basics...
Dont overthink.. I believe its pretty straight forward
and simple.
Lets asuume your Top file is top_entity and
your have a entity with a clock input.
Ex: entity top_entity is
port (
CLOCK :IN STD_LOGIC;
--Your other Port declarations
);
end top_entity;
--Your Architecure and the logic design follow
Just compile this top file of yours
make sure you have no errors..
Once done go to assignments->Pin assignments
Check up your schematic to know the pin number
to which your say 50MHz is connected.
In Pin assignments just assign that pin number
to your entities CLOCK.
This is all I guess.....
I hope this is what you were strugling with...